Workshops

Current Workshops

The TCBG is pleased to announce an upcoming Hands-on Workshop to be held at the Beckman Institute at the University of Illinois at Urbana, Champaign, on April 6-10, 2015.
This workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. Topics covered include: using VMD and NAMD, applications of VMD and NAMD in modern research, force fields and parameterizing new molecules, simulating membrane proteins and ion channels, modeling nucleic acid systems, computational nano-bio, evolutionary algorithms and network dynamics. Lectures in the morning will by followed by hands-on tutorials.

Prior Workshops

Computational Biophysics

Modeling the molecular processes of biological cells is
a craft and an art. Techniques like theoretical and computational skills can be
learnt by training, but meaningful applications are achieved only with
experience and sensitivity. The Theoretical and Computational Biophysics Group
has produced a series of workshops, attempting to teach both the craft and art of
modeling through learning by doing. Participants learn how to stretch proteins, pull water through
molecular channels, mine genomic data, and study their favorite biomolecules.
After lectures and discussions in the morning, afternoons are devoted to
hands-on computer laboratories where participants delved into hundreds of pages of
tutorials, on laptops humming with computational biology software, e.g.,
VMD and
NAMD. Learn more about each workshop by following the links below:

A workshop of about two days in length designed for researchers in computational and/or biophysical fields who seek to extend their GPU programming skills to include molecular modeling. The workshop extends GPU programming techniques to the field of molecular modeling, including subjects such as particle-grid algorithms (electrostatics and molecular orbitals), particle-particle algorithms with an emphasis on non-bonded force calculations, radial distribution functions in GPU histogramming, single-node multi-GPU algorithms, and GPU clusters.

In online workshops, participants are provided with a recorded, streaming video of a workshop lecture provided by TCBG faculty, along with the opportunity to complete tutorials with assistance from teaching assistants. Also provided is a conference call with the faculty member who provided the lecture, on the fourth and final date of the workshop.

The in-residence workshop program invites 5-7 scientists to the home of the TCBG for advanced training and consultation with an ongoing molecular dynamics study carried out by the participants. The in-residence training program provides an opportunity for experimentalists and theorists who are not experts in modeling, to initiate a project that requires advanced modeling. During their two-week stay, participants are provided with office space, use of computing facilities at the TCBG, and access to the expertise of TCBG group members. The goal of the in-residence workshop is to facilitate launch and refinement of participant modeling projects.

These day and a half workshops help users and
system administrators explore how to specify, design, build, and deploy PC
Clusters running Linux, and even determine if a cluster is right for a specific
application. Following a discussion of clustering basics, participants actually
built their own PC cluster and got to test out their own applications. The
workshops were aimed at systems administrators wanting a greater understanding
of cluster technologies, as well as those end-users that want to better
understand the systems that they work on for their day-to-day work. All cluster
building workshops were held in Urbana, Illinois, at the Beckman Institute.